Aligner Question

[jpjp]

Hi guys,

I am trying to develop an alignment software for paired end reads. But I can't find the values for the insert size and the standard deviation allowed in that value in the fastq file.

Is there a standard place where these values can be found? Could someone shed light on how other alignment software get these values?

thanks,

jp

[nilshomer]

Moved to the bioinformatics forum rather than posting to a thread that was a year old.

[rwenang]

CMIIW, the insert size depends on the wet-lab sequencing protocol / technology. So, if a bioinformatician were to use a mapping tool, they usually know the insert size in advance, either from the biologist, or from the protocol spec.

[jpjp]

thanks for the reply. I just thought if this information was part of the reads file (.fastq), that would be very natural.

[maubp]

The paired end insert size information is not in the FASTQ files (unless the sequencing center has a local convention via the read names, read descriptions, or filenames), nor in Roche 454's SFF files. The expected insert size is usually given separately (if you get told at all).

[krobison]

Many aligners simply infer it from the data; as mentioned above it depends on the protocol AND the actual size distribution may be different from what was expected.